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Table 3 Performances of the PhD-SNP and Meta-SNP on training set

From: Collective judgment predicts disease-associated single nucleotide variants

Dataset
(% of SV-2009)
Tool Q2 PPV TPR NPV TNR MCC AUC
SV-2009
(100%)
PhD-SNP 0.76 0.78 0.74 0.75 0.78 0.53 0.84
  Meta-SNP 0.79 0.80 0.79 0.79 0.80 0.59 0.87
Consensus
(46%)
PhD-SNP 0.87 0.87 0.92 0.87 0.79 0.73 0.89
  Meta-SNP 0.87 0.88 0.92 0.87 0.80 0.73 0.91
Majority
(40%)
PhD-SNP 0.70 0.67 0.56 0.72 0.80 0.37 0.77
  Meta-SNP 0.75 0.72 0.64 0.76 0.82 0.47 0.82
Tie
(14%)
PhD-SNP 0.61 0.51 0.43 0.66 0.73 0.16 0.67
  Meta-SNP 0.69 0.62 0.57 0.73 0.76 0.34 0.75
  1. Q2=Overall accuracy, PPV and NPV=Positive and Negative Predicted Values, TPR and TNR=True Positive and Negative Rates. MCC=Mathew's correlation, AUC=area under the (ROC) curve.